annotate emboss_getorf.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

<tool id="EMBOSS: getorf42" name="getorf" version="5.0.0.1">
  <description>Finds and extracts open reading frames (ORFs)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>getorf -sequence '$input1' -outseq '$out_file1' -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
  -osformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="table" type="select" label="Code to use">
      <option value="0">Standard</option>
      <option value="1">Standard (with alternative initiation codons)</option>
      <option value="2">Vertebrate Mitochondrial</option>
      <option value="3">Yeast Mitochondrial</option>
      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
      <option value="5">Invertebrate Mitochondrial</option>
      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
      <option value="9">Echinoderm Mitochondrial</option>
      <option value="10">Euplotid Nuclear</option>
      <option value="11">Bacterial</option>
      <option value="12">Alternative Yeast Nuclear</option>
      <option value="13">Ascidian Mitochondrial</option>
      <option value="14">Flatworm Mitochondrial</option>
      <option value="15">Blepharisma Macronuclear</option>
      <option value="16">Chlorophycean Mitochondrial</option>
      <option value="21">Trematode Mitochondrial</option>
      <option value="22">Scenedesmus obliquus</option>
      <option value="23">Thraustochytrium Mitochondrial</option>
    </param>
    <param name="minsize" type="integer" value="30" label="Minimum nucleotide size of ORF to report" />
    <param name="maxsize" type="integer" value="1000000" label="Maximum nucleotide size of ORF to report" />
    <param name="find" type="select" label="What to output">
      <option value="0">Translation of regions between STOP codons</option>
      <option value="1">Translation of regions between START and STOP codons</option>
      <option value="2">Nucleic sequences between STOP codons</option>
      <option value="3">Nucleic sequences between START and STOP codons</option>
      <option value="4">Nucleotides flanking START codons</option>
      <option value="5">Nucleotides flanking initial STOP codons</option>
      <option value="6">Nucleotides flanking ending STOP codons</option>
    </param>
    <param name="methionine" type="select" label="All START codons to code for Methionine">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="circular" type="select" label="Circular sequence">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="reverse" type="select" label="Find ORFs in the reverse complement">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="flanking" type="integer" value="100" label="Number of flanking nucleotides to output" />
    <param name="out_format1" type="select" label="Output sequence file format">
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>
      <option value="embl">EMBL (m)</option>
      <option value="fitch">Fitch (m)</option>
      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
      <option value="genbank">GENBANK (m)</option>
      <!-- <option value="gff">GFF (m)</option> -->
      <option value="hennig86">Hennig86 (m)</option>
      <option value="ig">Intelligenetics (m)</option>
      <option value="jackknifer">Jackknifer (m)</option>
      <option value="jackknifernon">Jackknifernon (m)</option>
      <option value="mega">Mega (m)</option>
      <option value="meganon">Meganon (m)</option>
      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
      <option value="pir">NBRF (PIR) (m)</option>
      <option value="ncbi">NCBI style FASTA (m)</option>
      <option value="nexus">Nexus/PAUP (m)</option>
      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
      <option value="phylip">PHYLIP interleaved (m)</option>
      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
      <option value="selex">SELEX (m)</option>
      <option value="staden">Staden (s)</option>
      <option value="strider">DNA strider (m)</option>
      <option value="swiss">SwisProt entry (m)</option>
      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="fasta" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minsize" value="30"/>
      <param name="maxsize" value="1000000"/>
      <param name="find" value="0"/>
      <param name="methionine" value="yes"/>
      <param name="circular" value="no"/>
      <param name="reverse" value="yes"/>
      <param name="table" value="0"/>
      <param name="flanking" value="100"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_getorf_out.fasta"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/getorf.html
  </help>
  <expand macro="citations" />
</tool>